After Gilbert Durandal gave his speech about how the world was manipulated by Logos, Earth's population rebelled against Logos and killed several of its members. The remaining members fled to Heaven's Base, which was then attacked by a combined force of ZAFT and defected Earth Alliance forces. Before the assault began Heaven's Base was given the ultimatum to hand over the members of Logos and dismantle. The ultimatum was answered by a barrage of rockets, signaling the start of the battle.

However Heaven's Base defense forces began to crumble when the ZAFT warship Minerva launched its ZGMF-X42S Destiny Gundam, ZGMF-X666S Legend Gundam, and ZGMF-X56S Impulse Gundam. The three suits quickly destroyed the five Destroy units. The loss of the Destroy mobile suits signified a turn in the battle, prompting Lord Djibril to evacuate. He was the only member of Logos to escape, the rest being captured and sentenced for their crimes. It is unknown what happened to the base after the battle.